OEDesignUnit

Attention

This API is currently available in C++ and Python.

class OEDesignUnit : public OESystem::OEBase

This is a container class derived from OEBase that holds all molecules needed to construct a model-ready biomolecular system.

Constructors

OEDesignUnit() -> OEDesignUnit
OEDesignUnit(rhs: OEDesignUnit) -> OEDesignUnit
OEDesignUnit(target: Union[OEGraphMol,OEMol,OEQMol],
             siteResidues: OEStringVector,
             solvent: Union[OEGraphMol,OEMol,OEQMol]=OEGraphMol(),
             cofactors: Union[OEGraphMol,OEMol,OEQMol]=OEGraphMol(),
             targetID: int) -> OEDesignUnit
OEDesignUnit(target: Union[OEGraphMol,OEMol,OEQMol],
             ligand: Union[OEGraphMol,OEMol,OEQMol],
             solvent: Union[OEGraphMol,OEMol,OEQMol]=OEGraphMol(),
             cofactors: Union[OEGraphMol,OEMol,OEQMol]=OEGraphMol(),
             targetID: int) -> OEDesignUnit

Default constructor.

Molecule constructors

Note

Molecule constructors are intended for already prepared molecules. They requires a target structure, as well as either a ligand or a list of binding site residues. Solvent and co-factors are optional, and are only set if the molecules passed are valid. The target molecule is not split into components and no structure preparation take place. A title will be generated based on the names of the provided molecules, but can be set manually afterwards.

OEDesignUnit(const OEChem::OEMolBase& target,
             const OEChem::OEMolBase& ligand,
             const OEChem::OEMolBase& solvent = OEChem::OEGraphMol(),
             const OEChem::OEMolBase& cofactors = OEChem::OEGraphMol(),
             const unsigned targetID = OEDesignUnitComponents::Protein)

Target-ligand constructor

OEDesignUnit(const OEChem::OEMolBase& target,
             const std::vector<std::string>& siteResidues,
             const OEChem::OEMolBase& solvent = OEChem::OEGraphMol(),
             const OEChem::OEMolBase& cofactors = OEChem::OEGraphMol(),
             const unsigned targetID = OEDesignUnitComponents::Protein)

Apo target constructor

operator=

Assignment operator.

operator bool

Clear

Clear() -> None

Resets the OEDesignUnit object to its initial state. This method deletes all internally stored molecules, and clears any OEBase data from the object.

CreateCopy

CreateCopy() -> OEDesignUnit

Deep copy constructor that returns a copy of the object. The memory for the returned OEDesignUnit object is dynamically allocated and owned by the caller.

GetComponent

GetComponent(molecule: Union[OEGraphMol,OEMol,OEQMol],
             componentID: int) -> bool

Returns a const reference to the molecule on the OEDesignUnit that is associated with the input componentID. Note that this function only works for single molecule components (e.g. protein, ligand, etc). This function requires an empty OEMolBase or it will clear the incoming molecule.

GetComponentID

GetComponentID(componentTag: str) -> int

Returns the internal unsigned integer representation of the componentTag string from the OEDesignUnit object.

GetComponentTag

GetComponentTag(componentID: int) -> str

Returns the string tag representation of the componentID unsigned integer from the OEDesignUnit object.

GetComponents

GetComponents(mol: Union[OEGraphMol,OEMol,OEQMol],
              componentMask: int, bondCovalent: bool = True,
              pred: OEUnaryAtomPred = OEIsTrueAtom()) -> bool

The function creates a single output mol from the components given in the componentMask bit mask. The bit mask can be constructed using unsigned integers stored in the OEDesignUnitComponents namespace. The function returns a boolean value to alert if the operation was successful. Note that this function only works for a list of components (e.g. other_ligands, excipients, etc). The optional predicate can be used to subset some of the components in the specified bit mask. The predicate does not have to be complete, e.g. two water molecules can be specified to subset the solvent category, but that will not subset the protein component also included in that mask. In essence the predicate is checked to see if it matches part of a design unit component and only in this case does it take effect.

GetComponentsWithin

GetComponentsWithin(mol: Union[OEGraphMol,OEMol,OEQMol],
                    componentMask: int, withinMask: int,
                    dist: float = 5.0, includeSelf: bool = False,
                    bondCovalent: bool = True) -> bool

The function creates a single output mol from the components given in the componentMask bit mask that fall within a dist distance of components given in the withinMask bit mask. All bit masks can be constructed using unsigned integers stored in the OEDesignUnitComponents namespace. If the boolean bondCovalent flag is set, all components that should be covalently bonded will have bonded added in the output mol. The function returns a boolean value to alert if the operation was successful.

GetDataType

GetDataType() -> void

This pure virtual function is used to perform run-time type identification. The value returned by the method should be equivalent to the value returned by OEGetDataType using the OEDesignUnit derived class type as the template argument.

GetIDs

GetIDs() -> OEUIntVector

Returns a vector of the component IDs stored on the OEDesignUnit object.

GetLigand

GetLigand(molecule: Union[OEGraphMol,OEMol,OEQMol]) -> bool

Returns success based on a valid copy of the ligand molecule in the OEDesignUnit object.

    lig = oechem.OEGraphMol()
    if not du.GetLigand(lig):
        oechem.OEThrow.Fatal("Error: Could not extract ligand from the OEDesignUnit.")
    oechem.OEWriteMolecule(ofs, lig)

Whole example script can be downloaded from here.

GetMetal

GetMetal(molecule: Union[OEGraphMol,OEMol,OEQMol]) -> bool

Returns success based on a valid copy of the metal in the OEDesignUnit object.

GetNucleicAcid

GetNucleicAcid(molecule: Union[OEGraphMol,OEMol,OEQMol]) -> bool

Returns success based on a valid copy of the nucleic acid molecule in the OEDesignUnit object.

GetPDBMetaData

GetPDBMetaData(mol: Union[OEGraphMol,OEMol,OEQMol]) -> bool

Returns success based on a valid copy of the PDB metadata in the OEDesignUnit object.

GetPackingResidues

GetPackingResidues(molecule: Union[OEGraphMol,OEMol,OEQMol]) -> bool

Returns success based on a valid copy of the packing residue molecule in the OEDesignUnit object.

GetProtein

GetProtein(molecule: Union[OEGraphMol,OEMol,OEQMol]) -> bool

Returns success based on a valid copy of the protein molecule in the OEDesignUnit object. Note that this function requires an empty OEMolBase or it will clear the incoming molecule.

GetReceptor

GetReceptor() -> OEReceptor

Returns a reference to the receptor on the OEDesignUnit object.

GetSiteResidues

GetSiteResidues() -> OEStringVector

Returns a vector of the site residue strings stored on the OEDesignUnit object. This function calls the OEResidueToString function with “:” delimiter.

GetSolvent

GetSolvent(molecule: Union[OEGraphMol,OEMol,OEQMol]) -> bool

Returns success based on a valid copy of the solvent molecule in the OEDesignUnit object.

GetStructureQuality

GetStructureQuality() -> OEStructureQuality

Returns the OEStructureQuality class stored on the OEDesignUnit object.

GetTransform

GetTransform(trans: OETrans) -> bool

Returns success based on a valid copy of the input OETrans object in the OEDesignUnit object.

GetTaggedComponents

GetTaggedComponents(componentMask: int) -> Iterable[Tuple[int, OEMolBase]]

Returns an OEIter of all molecules and corresponding molecular tags stored on the OEDesignUnit object. A bit mask of desired components can be constructed from constants in the OEDesignUnitComponents namespace and be passed in via the componentMask argument.

GetTags

GetTags() -> OEStringVector

Returns a vector of the tags of the molecules stored on the OEDesignUnit object.

GetTarget

GetTarget(molecule: Union[OEGraphMol,OEMol,OEQMol]) -> bool

Returns success based on a valid copy of the target molecule in the OEDesignUnit object.

GetTargetComponentID

GetTargetComponentID() -> int

Returns the component ID from the OEDesignUnitComponents namespace of the target molecule on the OEDesignUnit object.

GetTargetComponentTag

GetTargetComponentTag() -> str

Returns the string tag of the title of the OEDesignUnit object.

GetTitle

GetTitle() -> str

Returns the title of the OEDesignUnit object.

GetAltLoc

GetAltLoc() -> str

Returns the alternate location code used to generate the OEDesignUnit.

HasAltLoc

HasAltLoc(OEDesignUnit self) -> bool

Checks that the alternate locations flag on the OEDesignUnit object has been set.

HasComponent

HasComponent(componentID: int) -> bool

Checks that a molecule given by the componentID from the OEDesignUnitComponents namespace has been set on the OEDesignUnit object.

HasLigand

HasLigand() -> bool

Checks that the ligand molecule of the OEDesignUnit object has been set.

HasMetal

HasMetal() -> bool

Checks that the metal molecule of the OEDesignUnit object has been set.

HasNucleicAcid

HasNucleicAcid() -> bool

Checks that the nucleic acid molecule of the OEDesignUnit object has been set.

HasPDBMetaData

HasPDBMetaData() -> bool

Checks that the PDB metadata of the OEDesignUnit object has been set.

HasPackingResidues

HasPackingResidues() -> bool

Checks that the packing residue molecule of the OEDesignUnit object has been set.

HasProtein

HasProtein() -> bool

Checks that the protein molecule of the OEDesignUnit object has been set.

HasReceptor

HasReceptor() -> bool

Checks that the OEDesignUnit object contains a valid receptor.

HasSiteResidues

HasSiteResidues() -> bool

Checks that the site residues of the OEDesignUnit object has been set.

HasSolvent

HasSolvent() -> bool

Checks that the solvent molecule of the OEDesignUnit object has been set.

HasStructureQuality

HasStructureQuality() -> bool

Checks that the internal OEStructureQuality object stored on the OEDesignUnit has been set.

HasTransform

HasTransform() -> bool

Checks that the internal OETrans object stored on the OEDesignUnit has been set.

HasTarget

HasTitle

IsDataType

IsDataType(arg2: void) -> bool

Returns whether the type is the same as the instance this method is called on.

SetTitle

SetTitle(title: str) -> bool

Sets the title of the OEDesignUnit object.

SetSiteResidues

SetSiteResidues(siteResidues: OEResidueVector,
                threshold: float = 0.80, addBox: float = 2.0,
                rearrangeComponents: bool = False,
                siteSize: float = 5.0) -> bool

SetSiteResidues sets site residues from OEResidue objects, updates site-based components, and regenerates site-dependent interaction and style data.

SetSiteResidues requires residues that are present in the current target component. SetSiteResidues returns False if siteResidues is empty, or if any residue in siteResidues is not found in the target.

SetSiteResidues uses the optional parameters as follows:

The threshold option defines the minimum heavy-atom fraction of the current ligand that must fall inside the site box. Setting the value to 0.0 skips the ligand coverage validation.
The addBox option expands the site box before ligand coverage is evaluated.
The rearrangeComponents option controls whether components are re-arranged in the design unit based on whether the ligand coverage validation is true or false. Setting rearrangeComponents to False causes SetSiteResidues to return False when ligand coverage is below threshold. Setting the value to True, allows component reassignment when ligand coverage is below threshold. The current ligand is moved to OtherLigands and cofactors are moved to OtherCofactors. The list of OtherLigands is then evaluated, and the best ligand that meets threshold can be promoted into the ligand component, with corresponding OtherCofactors moved to the Cofactors component.
siteSize controls how site-associated cofactors are determined.

Note

SetSiteResidues preserves an existing receptor only when at least one new site residue overlaps the previous site-residue set. SetSiteResidues clears the receptor when no overlap is found.

ClearReceptor

ClearReceptor() -> bool

Clears the stored OEReceptor object.

ClearComponent
ClearComponent(componentTag: str, listIndex: int = -1) -> bool
ClearComponent(componentID: int, listIndex: int = -1) -> bool
Clears a specified component. The listIndex is intended for listComponents, e.g. co-factors. If the listIndex is -1 the entire list is removed, otherwise only the co-factor with the given index is removed.